AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i292_bsub_mtub_100.orf -o292_bsub_mtub_100.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -x5 -e Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 ycsF 204 similar to lactam utilization protein #2 ycsG 203 alternate gene name: ycsH; similar to branched chain amino acids transporter #3 ycsI 23 similar to hypothetical proteins #4 ycsJ 43 similar to allophanate hydrolase #5 Rv0264c 95 hypothetical protein Rv0264c #6 fecB2 21 fecB2 #7 Rv0266c 176 hypothetical protein Rv0266c Motif number 1 AAAAAGAGAGTCCTAAGATGGACT 1 2 1 AAAAGAGCCT 0.931266 -203 TGCCAAACTAAAAAGAGAGTCCATCTTAGGACT 1 19 0 AAAAGAGCCA 0.990709 -186 TGGTCCCAGAATAAAACCTGCCAAACTAAAAAG 1 37 0 AAAACCTCCA 0.947129 -168 TACTTTTGTCAGAAAACCTACCATGGTCCCAGA 1 60 0 AAAACCTCCA 0.947129 -145 CACTTATAATGAAATAAAGTTCAAAAATTCGGA 1 113 1 GAAAAAGTCA 0.875325 -92 GCAAAAAATCAGAAAACAGCTCAAAGCGGCTGG 2 74 1 AAAACAGTCA 0.967557 -130 CCTCTGTTCTGAAATAGCTGTCACTTCAATTCC 2 105 0 GAAAGCTTCA 0.959688 -99 CAGCTATTTCAGAACAGAGGTCAACATAAAGGA 2 118 1 AAAAGAGTCA 0.985337 -86 TGGAGCAGCAGAAAAAGACAGCAGGAAAAAAGC 2 162 1 GAAAGACGCA 0.926286 -42 AGACAGCAGGAAAAAAGCGGGCAGCTGGTCATT 2 177 1 AAAAGCGGCA 0.990905 -27 TATCTCCGCTGTAACAGCGCGCATCCGGGCCGG 7 83 0 GAAAGCGGCA 0.990281 -94 * ** **** *** Masking position 6 Map Score: 13.5641 Number of sites scoring better than the average of aligned sites = 448 Number in coding regions = 387 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 2 AGAATCCCTCCTGCCAAAGCAAACG 1 190 0 TCCTCCTGCC 0.991048 -15 GTCACTTCAATTCCAGCCGCTTTGAGCTGTT 2 88 0 TCCAGCCGCT 0.951009 -116 CTGCTGTCTTTTTCTGCTGCTCCATCTATTG 2 155 0 TTCTGCTGCT 0.959624 -49 GCCCGCTTTTTTCCTGCTGTCTTTTTCTGCT 2 168 0 TCCTGCTGTC 0.973844 -36 CAGCAATGACCAGCTGCCCGCTTTTTTC 2 186 0 GCCAGCTGCC 0.993906 -18 CGGTTAGGTCTCCTGTCGACAAGCGGG 7 7 1 GTCTCCTGTC 0.895694 -170 TTACCGCTGATGTCGCCCGCTTGTCGACAGG 7 22 0 TTCGCCCGCT 0.893081 -155 CCTGTTACCGGCCCGGATGCGCGCTGTTACA 7 76 1 GCCGGATGCG 0.952496 -101 GGTGGCTTCGGCCCGTCTGCCGTTGTGAGGA 7 122 1 GCCGTCTGCC 0.985787 -55 GTGAGGACGGGACCGGCTGCGAGCGTGAAGG 7 146 1 GCCGGCTGCG 0.994443 -31 * ********* Masking position 4 Map Score: 12.2469 Number of sites scoring better than the average of aligned sites = 1550 Number in coding regions = 1457 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 3 TGGAGATGGAGCCCATGCGCTGACATTTGCGCAA 2 44 1 GCCCCGCGAC 0.992873 -160 CTATTGTTCCTCCTTTATGTTGACCTCTGTTCTG 2 127 0 TCCTTGTGAC 0.859934 -77 AAAATCCCTGGCCGAGCCGAAGATTGCAGCGCTA 5 41 1 GCCGCGAGAT 0.959858 -55 GAAGATTGCAGCGCTACCGTCGACGCATGAGTGT 5 59 1 GCGCCGTGAC 0.98942 -37 CGCTGATGTCGCCCGCTTGTCGACAGGAGACCTA 7 15 0 GCCCTGTGAC 0.864169 -162 GGCGACATCAGCGGTAATGACGGCTCGACGCTAA 7 36 1 GCGGTGAGGC 0.740767 -141 CCTGTTACCGGCCCGGATGCGCGCTGTTACAGCG 7 76 1 GCCCTGCCGC 0.612427 -101 CGGCCCGTCTGCCGTTGTGAGGACGGGACCGGCT 7 130 1 GCCGTGAGAC 0.922592 -47 **** *** *** Masking position 9 Map Score: 6.53895 Number of sites scoring better than the average of aligned sites = 475 Number in coding regions = 448 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 4 GAGAGTCCTAAGATGGACTCTCTTTTTAGT 1 16 1 AGATGGACTC 0.946981 -189 TCATTTATGGAGATGGAGCCCATGCGCTGA 2 37 1 AGATGGAGCC 0.994654 -167 GTCAACATAAAGGAGGAACAATAGATGGAG 2 137 1 AGGAGGAACA 0.915548 -67 GAGGAACAATAGATGGAGCAGCAGAAAAAG 2 149 1 AGATGGAGCA 0.991621 -55 TATAAGTGGAGCAATTAAACAAA 3 4 1 AAGTGGAGCA 0.966434 -20 GCGAGCGTGAAGGGGGAGTCCGG 7 164 1 AGGGGGAGTC 0.978047 -13 ********** Masking position 7 Map Score: 4.48806 Number of sites scoring better than the average of aligned sites = 259 Number in coding regions = 207 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 5 TCTCTTTTTAGTTTGGCAGGTTTTATTCTG 1 34 1 GTTTGGCAGG 0.990774 -171 ATATCGTTTGCTTTGGCAGGAGGGATTCT 1 186 1 CTTTGGCAGG 0.996126 -19 GCTAAGGCACCTCTGGCAGTCTCGAAAATC 5 17 1 CTCTGGCAGT 0.991179 -79 CAATCTTCGGCTCGGCCAGGGATTTTCGAG 5 37 0 CTCGGCCAGG 0.975625 -59 ********** Masking position 8 Map Score: 3.01527 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 65 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 TCGACGCATGAGTGTGATGGACGTCTTT 5 78 1 AGTGTGATGG 0.989079 -18 AGCGTGAGGGTATCGCGCGC 6 12 0 AGCGTGAGGG 0.997276 -10 ACCGGCTGCGAGCGTGAAGGGGGAGTCCGG 7 157 1 AGCGTGAAGG 0.995968 -20 ********** Masking position 7 Map Score: 2.34872 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 23 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 7 AAAAAGAGAGTCCTAAGATGGACTCTCTT 1 10 1 GTCCTAAGAT 0.958437 -195 ACCTACCATGGTCCCAGAATAAAACCTGCC 1 48 0 GTCCCAGAAT 0.958535 -157 ATGAAATAAAGTTCAAAAATTCGGAATAGT 1 121 1 GTTCAAAAAT 0.905695 -84 GTCATTTATTGTCCCGAAATTCGGAACGAC 1 149 0 GTCCCGAAAT 0.985014 -56 GTTGACCTCTGTTCTGAAATAGCTGTCACT 2 113 0 GTTCTGAAAT 0.937381 -91 TCTTCGGCTCGGCCAGGGATTTTCGAGACT 5 34 0 GGCCAGGGAT 0.918079 -62 ********** Masking position 9 Map Score: 2.11967 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 151 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 8 AACTGATATGATTCACTTATAATGAAATAA 1 100 1 ATTCACTTAT 0.874329 -105 ATATGCTTTATGTCATTTATTGTCCCGAAA 1 160 0 TGTCATTTAT 0.979484 -45 TGTGTCATTTAAAAGCGGTTCA 2 3 1 TGTCATTTAA 0.970835 -201 GCGGTTCAGTTTTCATTTATGGAGATGGAG 2 25 1 TTTCATTTAT 0.954933 -179 CTGAAATAGCTGTCACTTCAATTCCAGCCG 2 100 0 TGTCACTTCA 0.941903 -104 ********** Masking position 5 Map Score: 1.57969 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 80 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 9 AATAAAACCTGCCAAACTAAAAAGAGAGTC 1 31 0 GCCAAACTAA 0.928457 -174 AATCCCTCCTGCCAAAGCAAACGATATGCT 1 183 0 GCCAAAGCAA 0.989965 -22 TGCCAGAGGTGCCTTAGCAAATGC 5 5 0 GCCTTAGCAA 0.944456 -91 AAAATCCCTGGCCGAGCCGAAGATTGCAGC 5 41 1 GCCGAGCCGA 0.965133 -55 CGGCAGACGGGCCGAAGCCACCTAAAGGTA 7 114 0 GCCGAAGCCA 0.988951 -63 ********** Masking position 10 Map Score: 0.660916 Number of sites scoring better than the average of aligned sites = 270 Number in coding regions = 251 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 10 CAATTCCAGCCGCTTTGAGCTGTTTTCTGA 2 82 0 CGCTTTGAGC 0.891079 -122 AGCAATGACCAGCTGCCCGCTTTTTTCCTG 2 183 0 AGCTGCCCGC 0.964772 -21 AGCGTGAGGGTATCGCGCGCG 6 4 0 GGTATCGCGC 0.930201 -18 GGGTCTCTTTAGCGTCGAGCCGTCATTACC 7 48 0 AGCGTCGAGC 0.964834 -129 TTACCGGCCCGGATGCGCGCTGTTACAGCG 7 80 1 GGATGCGCGC 0.984894 -97 ACCTTTAGGTGGCTTCGGCCCGTCTGCCGT 7 115 1 GGCTTCGGCC 0.960008 -62 GGACGGGACCGGCTGCGAGCGTGAAGGGGG 7 150 1 GGCTGCGAGC 0.996064 -27 ********** Masking position 2 Map Score: 3.49679 Number of sites scoring better than the average of aligned sites = 697 Number in coding regions = 657 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 11 ********** No masking Map Score: 9.40348e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 12 ********** No masking Map Score: 9.40348e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 13 ********** No masking Map Score: 9.40348e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0